Comparative genomic hybridization (CGH) is one approach that has been employed to detect the presence and identify the location of amplified or deleted sequences in a genome. In one implementation of CGH, genomic DNA is isolated from normal reference cells, as well as from test cells. The two genomic DNAs are differentially labeled and then simultaneously hybridized to an array of surface-bound polynucleotide probes, e.g., an array of BACs, cDNAs or oligonucleotides. Chromosomal regions in the test cells which are at increased or decreased copy number can be identified by detecting regions where the ratio of signal from the two distinguishably labeled nucleic acids is altered. For example, those regions that have been decreased in copy number in the test cells will show relatively lower signal from the test nucleic acid than the reference compared to other regions of the genome. Regions that have been increased in copy number in the test cells will show relatively higher signal from the test nucleic acid.